张贝 (2022-03-31 00:05):
#paper doi: 10.1038/s41586-021-03828-1 Nature, 2021, Highly accurate protein structure prediction for the human proteome. AlphaFold2是由DeepMind公司开发的人工智能系统,能够基于氨基酸序列,精确预测蛋白质的3D结构。预测的准确性可以与使用冷冻电镜、X射线衍射等手段解析的3D结构相媲美。AlphaFold2与基础版本相比,在蛋白结构解析的速度方面提升约16倍。本文利用AlphaFold2对98.5%的人类蛋白进行结构预测,并将预测的结果免费向公众开放。AlphaFold2能对人类蛋白质组58%的氨基酸的结构位置给出可信预测,且能对蛋白复合体的结构进行较好预测,其中低置信度的预测结果可能代表蛋白结构的无序状态。AlphaFold的出现代表人工智能驱动的生物学研究时代的来临。
IF:50.500Q1 Nature, 2021-08. DOI: 10.1038/s41586-021-03828-1 PMID: 34293799 PMCID:PMC8387240
Highly accurate protein structure prediction for the human proteome
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Abstract:
Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. After decades of effort, 17% of the total residues in human protein sequences are covered by an experimentally determined structure. Here we markedly expand the structural coverage of the proteome by applying the state-of-the-art machine learning method, AlphaFold, at a scale that covers almost the entire human proteome (98.5% of human proteins). The resulting dataset covers 58% of residues with a confident prediction, of which a subset (36% of all residues) have very high confidence. We introduce several metrics developed by building on the AlphaFold model and use them to interpret the dataset, identifying strong multi-domain predictions as well as regions that are likely to be disordered. Finally, we provide some case studies to illustrate how high-quality predictions could be used to generate biological hypotheses. We are making our predictions freely available to the community and anticipate that routine large-scale and high-accuracy structure prediction will become an important tool that will allow new questions to be addressed from a structural perspective.
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